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https://www.readbyqxmd.com/read/28212566/genetic-characterization-of-polish-ccrcc-patients-somatic-mutation-analysis-of-pbrm1-bap1-and-kdmc5-genomic-snp-array-analysis-in-tumor-biopsy-and-preliminary-results-of-chromosome-aberrations-analysis-in-plasma-cell-free-dna
#1
Katarzyna Kluzek, Malgorzata I Srebniak, Weronika Majer, Agnieszka Ida, Tomasz Milecki, Kinga Huminska, Robert M van der Helm, Adrian Silesian, Tomasz M Wrzesinski, Jacek Wojciechowicz, Berna H Beverloo, Zbigniew Kwias, Hans A R Bluyssen, Joanna Wesoly
BACKGROUND: Mutation analysis and cytogenetic testing in clear cell renal cell carcinoma (ccRCC) is not yet implemented in a routine diagnostics of ccRCC. MATERIAL AND METHODS: We characterized the chromosomal alterations in 83 ccRCC tumors from Polish patients using whole genome SNP genotyping assay. Moreover, the utility of next generation sequencing of cell free DNA (cfDNA) in patients plasma as a potential tool for non-invasive cytogenetic analysis was tested...
February 15, 2017: Oncotarget
https://www.readbyqxmd.com/read/28212557/using-high-sensitivity-sequencing-for-the-detection-of-mutations-in-btk-and-plc%C3%AE-2-genes-in-cellular-and-cell-free-dna-and-correlation-with-progression-in-patients-treated-with-btk-inhibitors
#2
Adam Albitar, Wanlong Ma, Ivan DeDios, Jeffrey Estella, Inhye Ahn, Mohammed Farooqui, Adrian Wiestner, Maher Albitar
Patients with chronic lymphocytic leukemia (CLL) that develop resistance to Bruton tyrosine kinase (BTK) inhibitors are typically positive for mutations in BTK or phospholipase c gamma 2 (PLCγ2). We developed a high sensitivity (HS) assay utilizing wild-type blocking polymerase chain reaction achieved via bridged and locked nucleic acids. We used this high sensitivity assay in combination with Sanger sequencing and next generation sequencing (NGS) and tested cellular DNA and cell-free DNA (cfDNA) from patients with CLL treated with the BTK inhibitor, ibrutinib...
February 13, 2017: Oncotarget
https://www.readbyqxmd.com/read/28207933/chorionic-villus-sampling-in-the-cell-free-dna-aneuploidy-screening-era-careful-selection-criteria-can-maximise-the-clinical-utility-of-screening-and-invasive-testing
#3
Stefan C Kane, Karen L Reidy, Fiona Norris, Deborah L Nisbet, Louise H Kornman, Ricardo Palma-Dias
OBJECTIVES: To quantify the impact of cell-free DNA (cfDNA) screening on chorionic villus sampling (CVS) test indications and outcomes in a tertiary maternity service. METHODS: Retrospective cohort study of all CVS procedures performed for any indication on singleton pregnancies at The Royal Women's Hospital, Melbourne, and at Women's Ultrasound Melbourne, Australia, between August 2008 and February 2015. Karyotypes were classified according to pathogenicity and detectability by standard cell-free DNA screening panels...
February 16, 2017: Prenatal Diagnosis
https://www.readbyqxmd.com/read/28206709/women-who-choose-cfdna-testing-should-not-be-denied-1-st-trimester-anatomy-scan
#4
Zarko Alfirevic, Catia M Bilardo, Laurent J Salomon, Ann Tabor
It is important to acknowledge that modern antenatal care includes a variety of screening programmes. Each of them should be evaluated in their own right and, when clinical effectiveness is proven, integrated in the antenatal care in the most cost-effective fashion. Screening for common aneuploidies and fetal anomalies are two such programmes which are routinely offered world-wide. Both screening programmes include components that interact with each other which leads to a considerable confusion in the debate about their evaluation and implementation...
February 16, 2017: BJOG: An International Journal of Obstetrics and Gynaecology
https://www.readbyqxmd.com/read/28205231/analysis-of-ctdna-to-predict-prognosis-and-monitor-treatment-responses-in-metastatic-pancreatic-cancer-patients
#5
He Cheng, Chen Liu, Jiahao Jiang, Guopei Luo, Yu Lu, Kaizhou Jin, Meng Guo, Zhenzhen Zhang, Jin Xu, Liang Liu, Quanxing Ni, Xianjun Yu
Cell-free circulating tumor DNA (ctDNA) in plasma has been used as a potential noninvasive biomarker for various tumors. The current study was performed to evaluate the clinical implications of ctDNA detection in patients with metastatic pancreatic cancer. Firstly, we attempted to prospectively screen a panel of 60 genes in cell-free DNA (cfDNA) from ten metastatic pancreatic cancer patients via exome sequencing. Secondly, droplet digital PCR (ddPCR) was used to identify potential mutations in a cohort of 188 patients with metastatic pancreatic cancer...
February 16, 2017: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/28195541/assessment-of-egfr-mutation-status-using-cell-free-dna-from-bronchoalveolar-lavage-fluid
#6
Sojung Park, Jae Young Hur, Kye Young Lee, Jae Cheol Lee, Jin Kyung Rho, Sun Hwa Shin, Chang-Min Choi
BACKGROUND: Much attention has been focused on epidermal growth factor receptor (EGFR) mutation testing since the introduction of EGFR-tyrosine kinase inhibitors have improved survival in EGFR-positive lung cancer patients. Liquid biopsy using circulating tumor cells or cell-free DNA (cfDNA) has enabled less invasive testing, but requires a highly sensitive method. To date, liquid biopsy using bronchoalveolar lavage (BAL) fluid has rarely been used. METHODS: From 20 patients with lung adenocarcinoma, we isolated cfDNA from 20 samples of cell-free BAL fluid and 19 cell-free bronchial washing samples...
February 14, 2017: Clinical Chemistry and Laboratory Medicine: CCLM
https://www.readbyqxmd.com/read/28183140/correlation-between-pik3ca-mutations-in-cell-free-dna-and-everolimus-efficacy-in-hr-her2-advanced-breast-cancer-results-from-bolero-2
#7
Mary Ellen Moynahan, David Chen, Wei He, Patricia Sung, Aliaksandra Samoila, Daoqi You, Trusha Bhatt, Parul Patel, Francois Ringeisen, Gabriel N Hortobagyi, Jose Baselga, Sarat Chandarlapaty
BACKGROUND: The current analysis was performed to evaluate the impact of PIK3CA hotspot mutations on everolimus efficacy in BOLERO-2 participants, using cell-free DNA (cfDNA) from plasma samples collected at the time of patient randomisation. METHODS: PIK3CA H1047R, E545K, and E542K mutations in plasma-derived cfDNA were analysed by droplet digital PCR (ddPCR). Median PFS was estimated for patient subgroups defined by PIK3CA mutations in each treatment arm. RESULTS: Among 550 patients included in cfDNA analysis, median PFS in everolimus vs placebo arms was similar in patients with tumours that had wild-type or mutant PIK3CA (hazard ratio (HR), 0...
February 9, 2017: British Journal of Cancer
https://www.readbyqxmd.com/read/28180146/-i-think-we-ve-got-too-many-tests-prenatal-providers-reflections-on-ethical-and-clinical-challenges-in-the-practice-integration-of-cell-free-dna-screening
#8
B L Gammon, S A Kraft, M Michie, M Allyse
BACKGROUND: The recent introduction of cell-free DNA-based non-invasive prenatal screening (cfDNA screening) into clinical practice was expected to revolutionize prenatal testing. cfDNA screening for fetal aneuploidy has demonstrated higher test sensitivity and specificity for some conditions than conventional serum screening and can be conducted early in the pregnancy. However, it is not clear whether and how clinical practices are assimilating this new type of testing into their informed consent and counselling processes...
July 2016: Ethics, Medicine, and Public Health
https://www.readbyqxmd.com/read/28179313/comparative-study-of-mutations-in-single-nucleotide-polymorphism-loci-of-kras-and-braf-genes-in-patients-who-underwent-screening-colonoscopy-with-and-without-premalignant-intestinal-polyps
#9
Michail Galanopoulos, Ioannis S Papanikolaou, Eleni Zografos, Nikos Viazis, George Papatheodoridis, Dimitrios Karamanolis, Evangelos Marinos, Gerassimos J Mantzaris, Maria Gazouli
AIM: Our aim was to perform a comparison study of the mutation rate of V-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog (KRAS), and v-Raf murine sarcoma viral oncogene homolog-B (BRAF) genes between blood-based cell-free DNA (cfDNA), and tissue sample biopsies in individuals undergoing screening colonoscopy. MATERIALS AND METHODS: All specimens were collected from January 2015 to January 2016. A total of 92 blood samples and colonic biopsy specimens were collected from healthy individuals with no polyps undergoing screening colonoscopy (group A, n=35), patients with colorectal cancer (group B, n=27), and patients with neoplastic intestinal polyps (group C, n=30)...
2017: Anticancer Research
https://www.readbyqxmd.com/read/28170370/development-of-a-gene-panel-for-next-generation-sequencing-of-clinically-relevant-mutations-in-cell-free-dna-from-cancer-patients
#10
Umberto Malapelle, Clara Mayo de-Las-Casas, Danilo Rocco, Monica Garzon, Pasquale Pisapia, Nuria Jordana-Ariza, Maria Russo, Roberta Sgariglia, Caterina De Luca, Francesco Pepe, Alejandro Martinez-Bueno, Daniela Morales-Espinosa, María González-Cao, Niki Karachaliou, Santiago Viteri Ramirez, Claudio Bellevicine, Miguel Angel Molina-Vila, Rafael Rosell, Giancarlo Troncone
BACKGROUND: When tumour tissue is unavailable, cell-free DNA (cfDNA)can serve as a surrogate for genetic analyses. Because mutated alleles in cfDNA are usually below 1%, next-generation sequencing (NGS)must be narrowed to target only clinically relevant genes. In this proof-of-concept study, we developed a panel to use in ultra-deep sequencing to identify such mutations in cfDNA. METHODS: Our panel ('SiRe') covers 568 mutations in six genes (EGFR, KRAS, NRAS, BRAF, cKIT and PDGFRα)involved in non-small-cell lung cancer (NSCLC), gastrointestinal stromal tumour, colorectal carcinoma and melanoma...
February 7, 2017: British Journal of Cancer
https://www.readbyqxmd.com/read/28164563/cell-free-dna-and-procalcitonin-as-early-markers-of-complications-in-icu-patients-with-multiple-trauma-and-major-surgery
#11
Asmaa I Ahmed, Randa A Soliman, Shereif Samir
BACKGROUND: Cell free DNA (cfDNA) was recently suggested as a new marker of sepsis and poor outcome in ICU patients. Procalcitonin has also been the focus of attention as an early marker for systemic inflammation and sepsis. METHODS: cfDNA, procalcitonin (PCT), C-reactive protein (CRP), and lactate levels were measured in 30 ICU patients with multiple trauma or after major surgery on the first day of admission and on 5th and 7th days for PCT, CRP, and lactate. cfDNA was measured by real-time PCR, PCT by ELISA, CRP immunoturbidimetrically, and lactate spectrophotometrically...
December 1, 2016: Clinical Laboratory
https://www.readbyqxmd.com/read/28164530/investigation-of-efficacy-evaluation-comparison-of-cfdna-and-cea-in-colorectal-cancer
#12
Dan Yu, GuangYu An, LingLing Xu
BACKGROUND: To investigate the comparison of efficacy evaluation value for cell-free DNA (cfDNA) and CEA in advanced colorectal cancer. METHODS: A total of 40 patients with advanced colorectal cancer were enrolled in this study. By PCR Real-time, changes of plasma ALU247and ALU115 level as well as the cfDNA integrity (ALU247/ALU115) before and after chemotherapy were analyzed in patients with advanced colorectal cancer. Meanwhile, changes of CEA before and after chemotherapy were monitored to compare the efficacy evaluation value of cfDNA and the conventional CEA in the treatment of advanced colorectal cancer...
October 1, 2016: Clinical Laboratory
https://www.readbyqxmd.com/read/28164427/application-of-circulating-tumor-dna-in-prospective-clinical-oncology-trials-standardization-of-pre-analytical-conditions
#13
Lisanne F van Dessel, Nick Beije, Jean C A Helmijr, Silvia R Vitale, Jaco Kraan, Maxime P Look, Ronald de Wit, Stefan Sleijfer, Maurice P H M Jansen, John W M Martens, Martijn P J K Lolkema
Circulating tumor DNA (ctDNA) has emerged as a potential new biomarker with diagnostic, predictive and prognostic applications for various solid tumor types. Before beginning large prospective clinical trials to prove the added value of utilizing ctDNA in clinical practice, it is essential to investigate the effects of various pre-analytical conditions on the quality of cell-free DNA (cfDNA) in general and of ctDNA in particular in order to optimize and standardize these conditions. Whole blood samples were collected from patients with metastatic cancer bearing a known somatic variant...
February 6, 2017: Molecular Oncology
https://www.readbyqxmd.com/read/28158220/targeted-capture-enrichment-assay-for-non-invasive-prenatal-testing-of-large-and-small-size-sub-chromosomal-deletions-and-duplications
#14
Maria C Neofytou, Kyriakos Tsangaras, Elena Kypri, Charalambos Loizides, Marios Ioannides, Achilleas Achilleos, Petros Mina, Anna Keravnou, Carolina Sismani, George Koumbaris, Philippos C Patsalis
Noninvasive prenatal testing (NIPT) using whole genome and targeted sequencing has become increasingly accepted for clinical detection of Trisomy 21 and sex chromosome aneuploidies. Few studies have shown that sub-chromosomal deletions or duplications associated with genetic syndromes can also be detected in the fetus noninvasively. There are still limitations on these methodologies such as the detection of variants of unknown clinical significance, high number of false positives, and difficulties to detect small aberrations...
2017: PloS One
https://www.readbyqxmd.com/read/28153663/obesity-and-cell-free-dna-no-calls-is-there-an-optimal-gestational-age-at-time-of-sampling
#15
Mary C Livergood, Kay A Lechien, Amanda S Trudell
BACKGROUND: Cell-free DNA (cfDNA) screen failure or "no calls" occur in 1-12% of samples and are frustrating for both clinician and patient. The rate of "no call" has shown to have an inverse relationship with gestational age. Recent studies have shown an increased risk for "no calls" among obese women. OBJECTIVE: To determine the optimal gestational age (GA) for cfDNA among obese women. STUDY DESIGN: We performed a retrospective cohort study of women who underwent cfDNA at a single tertiary care center from 2011-2016...
January 28, 2017: American Journal of Obstetrics and Gynecology
https://www.readbyqxmd.com/read/28152506/detection-fidelity-of-ar-mutations-in-plasma-derived-cell-free-dna
#16
Alexa Goldstein, Patricia Valda Toro, Justin Lee, John L Silberstein, Mary Nakazawa, Ian Waters, Karen Cravero, David Chu, Rory L Cochran, Minsoo Kim, Daniel Shinn, Samantha Torquato, Robert M Hughes, Aparna Pallavajjala, Michael A Carducci, Channing J Paller, Samuel R Denmeade, Bruce Kressel, Bruce J Trock, Mario A Eisenberger, Emmanuel S Antonarakis, Ben H Park, Paula J Hurley
Somatic genetic alterations including copy number and point mutations in the androgen receptor (AR) are associated with resistance to therapies targeting the androgen/AR axis in patients with metastatic castration resistant prostate cancer (mCRPC). Due to limitations associated with biopsying metastatic lesions, plasma derived cell-free DNA (cfDNA) is increasingly being used as substrate for genetic testing. AR mutations detected by deep next generation sequencing (NGS) of cfDNA from patients with mCRPC have been reported at allelic fractions ranging from over 25% to below 1%...
January 31, 2017: Oncotarget
https://www.readbyqxmd.com/read/28149760/comparison-of-methods-for-circulating-cell-free-dna-isolation-using-blood-from-cancer-patients-impact-on-biomarker-testing
#17
Clara Pérez-Barrios, Irene Nieto-Alcolado, María Torrente, Carolina Jiménez-Sánchez, Virginia Calvo, Lourdes Gutierrez-Sanz, Magda Palka, Encarnación Donoso-Navarro, Mariano Provencio, Atocha Romero
BACKGROUND: The implementation of liquid biopsy for biomarker testing and response to treatment monitoring in cancer patients would presumable increase laboratory throughput, requiring the development of automated methods for circulating free DNA (cfDNA) isolation. METHODS: The present study compares the MagNA Pure Compact (MPC) Nucleic Acid Isolation Kit I and Maxwell(®) RSC (MR) ccfDNA Plasma Kit and the later with QIAamp Circulating Nucleid Acid (QCNA) Kit using 57 plasma samples from cancer patients...
December 2016: Translational Lung Cancer Research
https://www.readbyqxmd.com/read/28141602/genetic-signature-and-profiling-of-head-and-neck-cancer-where-do-we-stand
#18
Julia Paczkowska, Krzysztof Szyfter, Maciej Giefing, Malgorzata Wierzbicka
PURPOSE OF REVIEW: To focus on two novel aspects of head and neck squamous cell carcinoma (HNSCC) genetics of special interest: the epithelial-mesenchymal transition (EMT) process, an initial step in tumor progression that finally leads to metastasis formation, by explaining how genes as well as epigenetic factors control this process, and the new diagnostic options based on the analysis of circulating tumor cells (CTCs) and cell-free DNA (cfDNA) that could revolutionize diagnosis in the coming years...
January 30, 2017: Current Opinion in Otolaryngology & Head and Neck Surgery
https://www.readbyqxmd.com/read/28129709/profile-of-the-roche-cobas-%C3%A2-egfr-mutation-test-v2-for-non-small-cell-lung-cancer
#19
Umberto Malapelle, Rafael Sirera, Eloísa Jantus-Lewintre, Pablo Reclusa, Silvia Calabuig-Fariñas, Ana Blasco, Pasquale Pisapia, Christian Rolfo, Carlos Camps
The discovery of driver mutations in non-small cell lung cancer (NSCLC) has led to the development of genome-based personalized medicine. Fifteen to 20% of adenocarcinomas harbor an epidermal growth factor receptor (EGFR) activating mutation associated with responses to EGFR tyrosine kinase inhibitors (TKIs). Individual laboratories' expertise and the availability of appropriate equipment are valuable assets in predictive molecular pathology, although the choice of methods should be determined by the nature of the samples to be tested and whether the detection of only well-characterized EGFR mutations or rather, of all detectable mutations, is required...
January 27, 2017: Expert Review of Molecular Diagnostics
https://www.readbyqxmd.com/read/28111423/induction-chemotherapy-with-gemcitabine-and-cisplatin-followed-by-simultaneous-integrated-boost-intensity-modulated-radiotherapy-with-concurrent-gemcitabine-for-locally-advanced-unresectable-pancreatic-cancer-results-from-a-feasibility-study
#20
Sang Myung Woo, Min Kyeong Kim, Jungnam Joo, Kyong-Ah Yoon, Boram Park, Sang-Jae Park, Sung-Sik Han, Ju Hee Lee, Eun Kyung Hong, Yun-Hee Kim, Hae Moon, Sun-Young Kong, Tae Hyun Kim, Woo Jin Lee
Purpose: This study assessed the feasibility and compliance of induction chemotherapy with gemcitabine and cisplatin followed by simultaneous integrated boost-intensity modulated radiotherapy (SIB-IMRT) with concurrent gemcitabine in patients with locally advanced unresectable pancreatic cancer (LAPC). Materials and Methods: In this trial, patients received induction chemotherapy consisting of gemcitabine (1000 mg/m2) and cisplatin (25 mg/m2) on days 1, 8 and 15 of each treatment cycle...
January 19, 2017: Cancer Research and Treatment: Official Journal of Korean Cancer Association
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